- Perchlorate contamination of groundwater is a worldwide concern. The most cost efficient treatment for high concentrations is biological treatment. In order to improve and increase the acceptance of this treatment, there is a need to reduce the contact between micro organisms in the treatment unit and the final effluent. An ion exchange membrane bioreactor (IEMB), in which treated water is separated from the bioreactor, was suggested for this purpose. In this study, the IEMB's performance was studied at a concentration as high as 250 mg L−1 that were never studied before. In the bioreactor, glycerol was used as a low cost and nontoxic carbon and energy source for the reduction of perchlorate to chloride. We found that high perchlorate concentrations in the feed rendered the anion exchange membrane significantly less permeable to perchlorate. However, the presence of bacteria in the bio-compartment significantly increased the flux through the membrane by more than 25% in comparison to pure Donnan dialysis. In addition, the results suggested minimal secondary contamination (<3 mg C L−1) of the treated water with the optimum feed of carbon substrate. Our results show that IEMB can efficiently treat groundwater contaminated with perchlorate as high as 250 mg L−1.